From 72b2149f3f011d7d4c6fe861648d0b594ce2299e Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Sun, 19 May 2013 19:25:49 +0100 Subject: [PATCH] JAL-???? notes on summarisation and analysis of annotation tracks --- doc/AnnotationPostAnalysis.txt | 39 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 doc/AnnotationPostAnalysis.txt diff --git a/doc/AnnotationPostAnalysis.txt b/doc/AnnotationPostAnalysis.txt new file mode 100644 index 0000000..f53533f --- /dev/null +++ b/doc/AnnotationPostAnalysis.txt @@ -0,0 +1,39 @@ +Init. +optimise rendering - use same model as alignment but with vertical binary sweep to select range of annotation to render: +Vertical interval list +. run length compress the sizes -> n_i * v_height_i -> label each node - total and accumulated total vertical pos (under current visibility settings ?) +--> ins/delete/hide/show of one or more contiguous individual rows causes local -> global update of position sums. +-- +. +indexOf(VPosition in annotation display window), +VPositionOf(AnnotationI) + +0. +i. Hide/show by whole annotation set id +ii. move to top/bottom +iii. + +1. Summarising annotation +{ Annotation Class ID +|_ { Type string } } +-> + +Simple modal : +- Proportion of sequences with most frequent symbol +- symbol logo +[ option to drill down and subselect based on particular symbol or subdivide by all symbols ] + +3. Clustering based on annotation +A few routes: +use built in PCA calculation to do scalar product based analysis of one or many annotation vectors. +Sliding window over alignment doing pca at each point. Analyse trajectories through PCA ? (see maximum/minimum and stretches of local similarity) + + +* ''' ACCESS ALL MENUS ''' +-> allow context popup to show all window submenus +{ local relevant } +{ Parent window -> file,edit,etc } +{ Desktop -> File, Tools, ... } +{ other areas more distant - e.g. sequence/annotation ID popup from middle of alignment/annotation area } + + \ No newline at end of file -- 1.7.10.2